I have no deals or treaties with this civilization, yet it seems like the computer is able to fly whatever type of fleet it wants through my territory, and even orbit my systems.

Even if I try to fly a ship into its territory I can't, as we don't have an open border treaty. Actually, if our relationship trend means anything, we are on the brink of war.

In the example below it looks like a couple of scouts, but sometimes Amoeba will fly massive groups of fleets across my territories that could easily wipe me out.
I am green. Yellow is clearly invading my territory.

1 Answer
1

Once a faction has the off string travel, it can travel through any territory, regardless of treaty status, to reach its destination, so long as it is traveling off-string. In your posted example picture, the Ameobas are traveling "off-string".

There was a bug in the game that allowed anyone to travel on-string regardless of treaty status as long as the destination was an unexplored star.